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I had the same thing happen to me I felt fine while on the meds and like carp after the meds. The was back in December now I have gastritis flareups and some burning when I have the flares especially if I eat certain things. My Dr said it takes months to get the stomach back on track. Remember the meds kill the good and bad bacterium so u need to get some probiotics to balance your stomach bac on track
I would call your physician and explain your symptoms and concerns.
This is probably due to the dying bugs giving off toxins as someone else says. If you continue to feel ill see your doctor and they will probably do a repeat H Pylori test to make sure all the bugs are gone. H Pylori can be tricky, sometimes it can come back, but don't worry it is easy to treat. You may just need another, maybe slightly longer, course of antibiotics.